Hey guys, I am using Mothur to analyse fungal 28S rRNA data. As there is no SOP for fungal 28S rRNA, I created my own taxonomy file according to LSURef_115_tax_silva_trunc.fasta (http://www.arb-silva.de/no_cache/download/archive/release_115/Exports/). I used Matlab to retrieve the sequnce name lines and made a taxonomy file corresponding to the fasta file.
However, it kept reminding me that seqs are in my template but not in the tax file. I looked up in my tax file and those missing seqs did exist.
This is my tax file looks like:
AAYL01000457.1.1925 Bacteria;Cyanobacteria;Chloroplast;
EF199972.1.3867 Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Collembola;Entomobryomorpha;Entomobryoidea;Entomobryidae;Orchesellinae;Orchesella;
Any suggestion is welcome. Thanks
Do you have the actual error message that you can send? Can you confirm that the number of lines in your fasta file is twice that of the number of lines in the tax file?
This is what I got:
‘CP000517.452641.455692’ is in your template file and is not in your taxonomy file. Please correct.
And I got this a lot.
The line number of tax file is 39412 while it’s 1477253 in fasta file. Maybe this causes the problem?
This is my fasta file looks like:
DQ150562.1.2440 Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Oxalobacteraceae;Herbaspirillum;Herbaspirillum autotrophicum
UAGGUCUGUG AGGCGAACGC GGCGAACUGA AACAUCUAAG UAGCUGCAGG AAAAGAAAUC AACCGAGAUU CCCAAAGUAG
UGGCGAGCGA AAUGGGACCA GCCUGCAAGA UUUAGCAUUU UUGAUAGUGG AACGGAAUGG AAAGUCCGGC CAUAGAGGGU
GAUAGCCCCU UACACGAAGU CAUUAGUGUG GAACUAGGCU UGCGACAAGU AGGGCGGGAC ACGUGAAAUC CUGUCUGAAC
AUGGGGGGAC CAUCCUCCAA GGCUAAAUAC UCGUAAUCGA CCGAUAGUGA ACCAGUACCG UGAGGGAAAG GCGAAAAGAA
CCCCGGAAGG GGAGUGAAAU AGAUCCUGAA ACCGUGUGCA UACAAACAGU AGGAGCCUCG CAAGGGGUGA CUGCGUACCU
UUUGUAUAAU GGGUCAGCGA CUUACAUUCA GUGGCAAGCU UAACCGAAUA GGGAAGGCGU AGAGAAAUCG AGUCCGAAUA
GGGCGUUCAG UCGCUGGGUG UAGACCCGAA ACCAAGUGAU CUACUCAUGG CCAGGUUGAA GGUGCGGUAA CACGCACUGG
AGGACCGAAC CCACUAAUGU UGAAAAAUUA GGGGAUGAGC UGUGGGUAGG GGUGAAAGGC UAAACAAACU UGGAAAUAGC
UGGUUCUCUC CGAAAACUAU UUAGGUAGUG CCUCAAGUAU CACCAUCGGG GGUAGAGCAC UGUUAUGGCU AGGGGGUCAU
CGCGACUUAC CAACCCAUUG CAAACUCCGA AUACCGAUGA GUGCGAGCUU GGGAGACAGA CGUCGGGUGC UAACGUCCGG
CGUCAAGAGG GAAACAACCC AGACCGCCAG CUAAGGUCCC AAAGAUUGGC UAAGUGGAAA ACGAAGUGGG AAGGCUAAAA
CAGUCAGGAG GUUGGCUUAG AAGCAGCCAU CCUUUAAAGA AAGCGUAAUA GCUCACUGAU CGAGUCGUCC UGCGCGGAAG
AUGUAACGGG GCUAAGCCAG UCACCGAAGC UGCGGAUAUC AAUUUAUUGA UAUGGUAGGA GAGCGUUCUG UAAGCCUGCG
AAGGUGUCUU GUAAAGGAUG CUGGAGGUAU CAGAAGUGCG AAUGCUGACA UGAGUAGCGA UAAUGGGGGU GAAAAGCCUC
CACGCCGUAA GCCCAAGGUU UCCUGUUCAA CGUUCAUCGG AGCAGGGUGA GUCGGCCCCU AAGGCGAGGC AGAGAUGCGU
AGCUGAUGGG AAGCAGGUUA AUAUUCCUGC ACCGUCGUUA GAUGCGAUGG GGGGACGGAU CGCGGAAGGU UGUCCGGGUG
UUGGAAGUCC CGGUUUCUGU AUCAGAGAAG GCUGUUAGGC AAAUCCGGCA GCGUAAUUCA AGGGUAUGGG ACGAGUGAAC
UUGUUCACGA AGCAAUCGGA AGUGGUUCCA AGAAAAGCCU CUAAGCUUCA GUCUAACGAG ACCGUACCGC AAACCGACAC
AGGUGGGCGA GAUGAGUAUU CUAAGGCGCU UGAGAGAACU CGGGAGAAGG AACUCGGCAA AUUUGUACCG UAACUUCGGG
AUAAGGUACG CCCUAGUAGU UUGACAGGCC UGCGCUUGAA GGACGAAAGG GUUGCAAUAA AAAGGUGGCU GCGACUGUUU
AAUAAAAACA CAGCACUCUG CAAACACGAA AGUGGACGUA UAGGGUGUGA CGCCUGCCUG GUGCUGGAAG AUUAAAUGAU
GGGGUGCAAG CUCUUGAUUG AAGUCCCAGU AAACGGCGGC CGUAACUAUA ACGGUCCUAA GGUAGCGAAA UUCCUUGUCG
GGUAAGUUCC GACCUGCACG AAUGGCGUAA CGAUGGCCAC ACUGUCUCCU CCCGAGACUC AGCGAAGUUG AAAUGUUUGU
GAUGAUGCAA UCUACCCGCG GCUAGACGGA AAGACCCCAU GAACCUUUAC UGUAGCUUUG CAUUGGACUU UGAACCAAUC
UGUGUAGGAU AGGUGGGAGG CUUUGAAGCG GGGACGCUAG UUCUCGUGGA GCCAUCCUUG AAAUACCACC CUGGUUUGUU
UGAGGUUCUA ACCUUGGUCC GUUAUCCGGA UCGGGGACAG UGCAUGGUAG GCAGUUUGAC UGGGGCGGUC UCCUCCCAAA
GUGUAACGGA GGAGUUCGAA GGUACGCUAG GUACGGUCGG ACAUCGUGCU AAUAGUGCAA UGGCAUAAGC GUGCUUAACU
GCGAGACUGA CAAGUCGAGC AGGUACGAAA GUAGGACAUA GUGAUCCGGU GGUUCUGUAU GGAAGGGCCA UCGCUCAACG
GAUAAAAGGU ACUCUGGGGA UAACAGGCUG AUUCCUCCCA AGAGUUCAUA UCGACGGGGG AGUUUGGCAC CUCGAUGUCG
GCUCAUCACA UCCUGGGGCU GUAGCCGGUC CCAAGGGUAU GGCUGUUCGC CAUUUAAAGU GGUACGUGAG CUGGGUUUAA
AACGUCGUGA GACAGUUUGG UCCCUAUCUG CCGUGGGCGU
Yeah you need one entry in the tax file for every one in the fasta file. Plus they all need to have unique sequence names.
Pat